Load scripts: loads libraries and useful scripts used in the analyses; all .R files contained in scripts at the root of the factory are automatically loaded
Load data: imports datasets, and may contain some ad hoc changes to the data such as specific data cleaning (not used in other reports), new variables used in the analyses, etc.
library(reportfactory)
library(here)
library(rio)
library(tidyverse)
library(incidence)
library(distcrete)
library(epitrix)
library(earlyR)
library(projections)
library(linelist)
library(remotes)
library(janitor)
library(kableExtra)
library(DT)
library(cyphr)
library(chngpt)
library(lubridate)
library(ggpubr)
library(ggnewscale)These scripts will load:
.R files inside /scripts/.R files inside /src/These scripts also contain routines to access the latest clean encrypted data (see next section).
We import the latest NHS pathways data:
x <- import_pathways() %>%
as_tibble()
x
## [90m# A tibble: 163,936 x 11[39m
## site_type date sex age ccg_code ccg_name count postcode nhs_region
## [3m[90m<chr>[39m[23m [3m[90m<date>[39m[23m [3m[90m<chr>[39m[23m [3m[90m<chr>[39m[23m [3m[90m<chr>[39m[23m [3m[90m<chr>[39m[23m [3m[90m<int>[39m[23m [3m[90m<chr>[39m[23m [3m[90m<chr>[39m[23m
## [90m 1[39m 111 2020-03-18 fema… 70-1… e380000… nhs_cas… 6 ss67qf East of E…
## [90m 2[39m 111 2020-03-18 fema… 70-1… e380000… nhs_cho… 1 pr266tt North West
## [90m 3[39m 111 2020-03-18 fema… 70-1… e380000… nhs_dor… 5 dt11tg South West
## [90m 4[39m 111 2020-03-18 fema… 70-1… e380000… nhs_dud… 5 dy51ru Midlands
## [90m 5[39m 111 2020-03-18 fema… 70-1… e380000… nhs_eas… 2 de142wf Midlands
## [90m 6[39m 111 2020-03-18 fema… 70-1… e380000… nhs_hul… 4 hu11uy North Eas…
## [90m 7[39m 111 2020-03-18 fema… 70-1… e380000… nhs_har… 1 ha13aw London
## [90m 8[39m 111 2020-03-18 fema… 70-1… e380000… nhs_ham… 1 dl62uu North Eas…
## [90m 9[39m 111 2020-03-18 fema… 70-1… e380000… nhs_gre… 2 se186nd London
## [90m10[39m 111 2020-03-18 fema… 19-69 w110000… null 1 [31mNA[39m [31mNA[39m
## [90m# … with 163,926 more rows, and 2 more variables: day [3m[90m<int>[90m[23m, weekday [3m[90m<fct>[90m[23m[39mWe also import demographics data for NHS regions in England, used later in our analysis:
path <- here::here("data", "csv", "nhs_region_population_2018.csv")
nhs_region_pop <- rio::import(path) %>%
mutate(nhs_region = str_to_title(gsub("_"," ",nhs_region)))
nhs_region_pop$nhs_region <- gsub(" Of ", " of ", nhs_region_pop$nhs_region)
nhs_region_pop$nhs_region <- gsub(" And ", " and ", nhs_region_pop$nhs_region)
nhs_region_pop
## nhs_region variable value
## 1 North West 0-18 0.22538599
## 2 North East and Yorkshire 0-18 0.21876449
## 3 Midlands 0-18 0.22564656
## 4 East of England 0-18 0.22810783
## 5 London 0-18 0.23764782
## 6 South East 0-18 0.22458811
## 7 South West 0-18 0.20799797
## 8 North West 19-69 0.64274078
## 9 North East and Yorkshire 19-69 0.64437753
## 10 Midlands 19-69 0.63876675
## 11 East of England 19-69 0.63034229
## 12 London 19-69 0.67820084
## 13 South East 19-69 0.63267336
## 14 South West 19-69 0.63176131
## 15 North West 70-120 0.13187323
## 16 North East and Yorkshire 70-120 0.13685797
## 17 Midlands 70-120 0.13558669
## 18 East of England 70-120 0.14154988
## 19 London 70-120 0.08415135
## 20 South East 70-120 0.14273853
## 21 South West 70-120 0.16024072Finally, we import publically available deaths per NHS region:
dth <- import_deaths() %>%
mutate(nhs_region = str_to_title(gsub("_"," ",nhs_region)))
#truncation to account for reporting delay
delay_max <- 21
dth$nhs_region <- gsub(" Of ", " of ", dth$nhs_region)
dth$nhs_region <- gsub(" And ", " and ", dth$nhs_region)
dth
## date_report nhs_region deaths
## 1 2020-03-01 East of England 0
## 2 2020-03-02 East of England 1
## 3 2020-03-03 East of England 0
## 4 2020-03-04 East of England 0
## 5 2020-03-05 East of England 0
## 6 2020-03-06 East of England 1
## 7 2020-03-07 East of England 0
## 8 2020-03-08 East of England 0
## 9 2020-03-09 East of England 1
## 10 2020-03-10 East of England 0
## 11 2020-03-11 East of England 0
## 12 2020-03-12 East of England 0
## 13 2020-03-13 East of England 1
## 14 2020-03-14 East of England 2
## 15 2020-03-15 East of England 2
## 16 2020-03-16 East of England 1
## 17 2020-03-17 East of England 1
## 18 2020-03-18 East of England 5
## 19 2020-03-19 East of England 4
## 20 2020-03-20 East of England 2
## 21 2020-03-21 East of England 11
## 22 2020-03-22 East of England 12
## 23 2020-03-23 East of England 11
## 24 2020-03-24 East of England 19
## 25 2020-03-25 East of England 26
## 26 2020-03-26 East of England 36
## 27 2020-03-27 East of England 38
## 28 2020-03-28 East of England 28
## 29 2020-03-29 East of England 43
## 30 2020-03-30 East of England 45
## 31 2020-03-31 East of England 70
## 32 2020-04-01 East of England 62
## 33 2020-04-02 East of England 64
## 34 2020-04-03 East of England 80
## 35 2020-04-04 East of England 71
## 36 2020-04-05 East of England 76
## 37 2020-04-06 East of England 71
## 38 2020-04-07 East of England 93
## 39 2020-04-08 East of England 111
## 40 2020-04-09 East of England 87
## 41 2020-04-10 East of England 74
## 42 2020-04-11 East of England 92
## 43 2020-04-12 East of England 101
## 44 2020-04-13 East of England 78
## 45 2020-04-14 East of England 61
## 46 2020-04-15 East of England 82
## 47 2020-04-16 East of England 74
## 48 2020-04-17 East of England 86
## 49 2020-04-18 East of England 64
## 50 2020-04-19 East of England 67
## 51 2020-04-20 East of England 67
## 52 2020-04-21 East of England 75
## 53 2020-04-22 East of England 67
## 54 2020-04-23 East of England 49
## 55 2020-04-24 East of England 66
## 56 2020-04-25 East of England 54
## 57 2020-04-26 East of England 48
## 58 2020-04-27 East of England 46
## 59 2020-04-28 East of England 58
## 60 2020-04-29 East of England 32
## 61 2020-04-30 East of England 45
## 62 2020-05-01 East of England 49
## 63 2020-05-02 East of England 29
## 64 2020-05-03 East of England 41
## 65 2020-05-04 East of England 19
## 66 2020-05-05 East of England 36
## 67 2020-05-06 East of England 31
## 68 2020-05-07 East of England 33
## 69 2020-05-08 East of England 33
## 70 2020-05-09 East of England 29
## 71 2020-05-10 East of England 22
## 72 2020-05-11 East of England 18
## 73 2020-05-12 East of England 21
## 74 2020-05-13 East of England 27
## 75 2020-05-14 East of England 26
## 76 2020-05-15 East of England 19
## 77 2020-05-16 East of England 26
## 78 2020-05-17 East of England 17
## 79 2020-05-18 East of England 25
## 80 2020-05-19 East of England 15
## 81 2020-05-20 East of England 26
## 82 2020-05-21 East of England 21
## 83 2020-05-22 East of England 13
## 84 2020-05-23 East of England 12
## 85 2020-05-24 East of England 17
## 86 2020-05-25 East of England 25
## 87 2020-05-26 East of England 14
## 88 2020-05-27 East of England 12
## 89 2020-05-28 East of England 17
## 90 2020-05-29 East of England 16
## 91 2020-05-30 East of England 9
## 92 2020-05-31 East of England 8
## 93 2020-06-01 East of England 17
## 94 2020-06-02 East of England 14
## 95 2020-06-03 East of England 10
## 96 2020-06-04 East of England 7
## 97 2020-06-05 East of England 12
## 98 2020-06-06 East of England 5
## 99 2020-06-07 East of England 9
## 100 2020-06-08 East of England 5
## 101 2020-06-09 East of England 6
## 102 2020-06-10 East of England 8
## 103 2020-06-11 East of England 1
## 104 2020-06-12 East of England 9
## 105 2020-06-13 East of England 5
## 106 2020-06-14 East of England 4
## 107 2020-06-15 East of England 8
## 108 2020-06-16 East of England 3
## 109 2020-06-17 East of England 7
## 110 2020-06-18 East of England 4
## 111 2020-06-19 East of England 7
## 112 2020-06-20 East of England 3
## 113 2020-06-21 East of England 3
## 114 2020-06-22 East of England 6
## 115 2020-06-23 East of England 4
## 116 2020-06-24 East of England 4
## 117 2020-06-25 East of England 1
## 118 2020-06-26 East of England 4
## 119 2020-06-27 East of England 5
## 120 2020-06-28 East of England 5
## 121 2020-06-29 East of England 4
## 122 2020-06-30 East of England 0
## 123 2020-03-01 London 0
## 124 2020-03-02 London 0
## 125 2020-03-03 London 0
## 126 2020-03-04 London 0
## 127 2020-03-05 London 0
## 128 2020-03-06 London 1
## 129 2020-03-07 London 0
## 130 2020-03-08 London 0
## 131 2020-03-09 London 1
## 132 2020-03-10 London 0
## 133 2020-03-11 London 6
## 134 2020-03-12 London 6
## 135 2020-03-13 London 10
## 136 2020-03-14 London 14
## 137 2020-03-15 London 10
## 138 2020-03-16 London 15
## 139 2020-03-17 London 23
## 140 2020-03-18 London 27
## 141 2020-03-19 London 25
## 142 2020-03-20 London 44
## 143 2020-03-21 London 49
## 144 2020-03-22 London 54
## 145 2020-03-23 London 63
## 146 2020-03-24 London 87
## 147 2020-03-25 London 113
## 148 2020-03-26 London 129
## 149 2020-03-27 London 130
## 150 2020-03-28 London 122
## 151 2020-03-29 London 146
## 152 2020-03-30 London 149
## 153 2020-03-31 London 181
## 154 2020-04-01 London 202
## 155 2020-04-02 London 191
## 156 2020-04-03 London 196
## 157 2020-04-04 London 230
## 158 2020-04-05 London 195
## 159 2020-04-06 London 197
## 160 2020-04-07 London 220
## 161 2020-04-08 London 238
## 162 2020-04-09 London 206
## 163 2020-04-10 London 170
## 164 2020-04-11 London 178
## 165 2020-04-12 London 158
## 166 2020-04-13 London 166
## 167 2020-04-14 London 144
## 168 2020-04-15 London 142
## 169 2020-04-16 London 139
## 170 2020-04-17 London 100
## 171 2020-04-18 London 101
## 172 2020-04-19 London 103
## 173 2020-04-20 London 95
## 174 2020-04-21 London 94
## 175 2020-04-22 London 109
## 176 2020-04-23 London 77
## 177 2020-04-24 London 71
## 178 2020-04-25 London 58
## 179 2020-04-26 London 53
## 180 2020-04-27 London 51
## 181 2020-04-28 London 43
## 182 2020-04-29 London 44
## 183 2020-04-30 London 40
## 184 2020-05-01 London 41
## 185 2020-05-02 London 41
## 186 2020-05-03 London 36
## 187 2020-05-04 London 30
## 188 2020-05-05 London 25
## 189 2020-05-06 London 37
## 190 2020-05-07 London 37
## 191 2020-05-08 London 30
## 192 2020-05-09 London 23
## 193 2020-05-10 London 26
## 194 2020-05-11 London 18
## 195 2020-05-12 London 18
## 196 2020-05-13 London 16
## 197 2020-05-14 London 20
## 198 2020-05-15 London 18
## 199 2020-05-16 London 14
## 200 2020-05-17 London 15
## 201 2020-05-18 London 9
## 202 2020-05-19 London 14
## 203 2020-05-20 London 19
## 204 2020-05-21 London 12
## 205 2020-05-22 London 10
## 206 2020-05-23 London 6
## 207 2020-05-24 London 7
## 208 2020-05-25 London 9
## 209 2020-05-26 London 13
## 210 2020-05-27 London 7
## 211 2020-05-28 London 8
## 212 2020-05-29 London 7
## 213 2020-05-30 London 12
## 214 2020-05-31 London 6
## 215 2020-06-01 London 10
## 216 2020-06-02 London 7
## 217 2020-06-03 London 6
## 218 2020-06-04 London 8
## 219 2020-06-05 London 4
## 220 2020-06-06 London 0
## 221 2020-06-07 London 5
## 222 2020-06-08 London 5
## 223 2020-06-09 London 4
## 224 2020-06-10 London 7
## 225 2020-06-11 London 5
## 226 2020-06-12 London 3
## 227 2020-06-13 London 3
## 228 2020-06-14 London 2
## 229 2020-06-15 London 1
## 230 2020-06-16 London 2
## 231 2020-06-17 London 1
## 232 2020-06-18 London 2
## 233 2020-06-19 London 3
## 234 2020-06-20 London 3
## 235 2020-06-21 London 4
## 236 2020-06-22 London 2
## 237 2020-06-23 London 0
## 238 2020-06-24 London 3
## 239 2020-06-25 London 3
## 240 2020-06-26 London 2
## 241 2020-06-27 London 1
## 242 2020-06-28 London 1
## 243 2020-06-29 London 2
## 244 2020-06-30 London 0
## 245 2020-03-01 Midlands 0
## 246 2020-03-02 Midlands 0
## 247 2020-03-03 Midlands 1
## 248 2020-03-04 Midlands 0
## 249 2020-03-05 Midlands 0
## 250 2020-03-06 Midlands 0
## 251 2020-03-07 Midlands 0
## 252 2020-03-08 Midlands 3
## 253 2020-03-09 Midlands 1
## 254 2020-03-10 Midlands 0
## 255 2020-03-11 Midlands 2
## 256 2020-03-12 Midlands 6
## 257 2020-03-13 Midlands 5
## 258 2020-03-14 Midlands 4
## 259 2020-03-15 Midlands 5
## 260 2020-03-16 Midlands 11
## 261 2020-03-17 Midlands 8
## 262 2020-03-18 Midlands 13
## 263 2020-03-19 Midlands 8
## 264 2020-03-20 Midlands 28
## 265 2020-03-21 Midlands 13
## 266 2020-03-22 Midlands 31
## 267 2020-03-23 Midlands 33
## 268 2020-03-24 Midlands 41
## 269 2020-03-25 Midlands 48
## 270 2020-03-26 Midlands 64
## 271 2020-03-27 Midlands 72
## 272 2020-03-28 Midlands 89
## 273 2020-03-29 Midlands 92
## 274 2020-03-30 Midlands 90
## 275 2020-03-31 Midlands 123
## 276 2020-04-01 Midlands 140
## 277 2020-04-02 Midlands 142
## 278 2020-04-03 Midlands 124
## 279 2020-04-04 Midlands 151
## 280 2020-04-05 Midlands 164
## 281 2020-04-06 Midlands 140
## 282 2020-04-07 Midlands 123
## 283 2020-04-08 Midlands 186
## 284 2020-04-09 Midlands 139
## 285 2020-04-10 Midlands 127
## 286 2020-04-11 Midlands 142
## 287 2020-04-12 Midlands 139
## 288 2020-04-13 Midlands 120
## 289 2020-04-14 Midlands 116
## 290 2020-04-15 Midlands 147
## 291 2020-04-16 Midlands 102
## 292 2020-04-17 Midlands 118
## 293 2020-04-18 Midlands 115
## 294 2020-04-19 Midlands 92
## 295 2020-04-20 Midlands 107
## 296 2020-04-21 Midlands 86
## 297 2020-04-22 Midlands 78
## 298 2020-04-23 Midlands 103
## 299 2020-04-24 Midlands 79
## 300 2020-04-25 Midlands 72
## 301 2020-04-26 Midlands 81
## 302 2020-04-27 Midlands 74
## 303 2020-04-28 Midlands 68
## 304 2020-04-29 Midlands 53
## 305 2020-04-30 Midlands 56
## 306 2020-05-01 Midlands 64
## 307 2020-05-02 Midlands 51
## 308 2020-05-03 Midlands 52
## 309 2020-05-04 Midlands 61
## 310 2020-05-05 Midlands 59
## 311 2020-05-06 Midlands 59
## 312 2020-05-07 Midlands 48
## 313 2020-05-08 Midlands 34
## 314 2020-05-09 Midlands 37
## 315 2020-05-10 Midlands 42
## 316 2020-05-11 Midlands 33
## 317 2020-05-12 Midlands 45
## 318 2020-05-13 Midlands 40
## 319 2020-05-14 Midlands 37
## 320 2020-05-15 Midlands 40
## 321 2020-05-16 Midlands 34
## 322 2020-05-17 Midlands 31
## 323 2020-05-18 Midlands 34
## 324 2020-05-19 Midlands 34
## 325 2020-05-20 Midlands 36
## 326 2020-05-21 Midlands 32
## 327 2020-05-22 Midlands 27
## 328 2020-05-23 Midlands 34
## 329 2020-05-24 Midlands 19
## 330 2020-05-25 Midlands 26
## 331 2020-05-26 Midlands 33
## 332 2020-05-27 Midlands 29
## 333 2020-05-28 Midlands 28
## 334 2020-05-29 Midlands 20
## 335 2020-05-30 Midlands 20
## 336 2020-05-31 Midlands 22
## 337 2020-06-01 Midlands 20
## 338 2020-06-02 Midlands 22
## 339 2020-06-03 Midlands 24
## 340 2020-06-04 Midlands 16
## 341 2020-06-05 Midlands 21
## 342 2020-06-06 Midlands 20
## 343 2020-06-07 Midlands 17
## 344 2020-06-08 Midlands 16
## 345 2020-06-09 Midlands 18
## 346 2020-06-10 Midlands 15
## 347 2020-06-11 Midlands 13
## 348 2020-06-12 Midlands 12
## 349 2020-06-13 Midlands 6
## 350 2020-06-14 Midlands 18
## 351 2020-06-15 Midlands 12
## 352 2020-06-16 Midlands 14
## 353 2020-06-17 Midlands 10
## 354 2020-06-18 Midlands 14
## 355 2020-06-19 Midlands 9
## 356 2020-06-20 Midlands 14
## 357 2020-06-21 Midlands 12
## 358 2020-06-22 Midlands 12
## 359 2020-06-23 Midlands 17
## 360 2020-06-24 Midlands 13
## 361 2020-06-25 Midlands 15
## 362 2020-06-26 Midlands 5
## 363 2020-06-27 Midlands 3
## 364 2020-06-28 Midlands 5
## 365 2020-06-29 Midlands 4
## 366 2020-06-30 Midlands 0
## 367 2020-03-01 North East and Yorkshire 0
## 368 2020-03-02 North East and Yorkshire 0
## 369 2020-03-03 North East and Yorkshire 0
## 370 2020-03-04 North East and Yorkshire 0
## 371 2020-03-05 North East and Yorkshire 0
## 372 2020-03-06 North East and Yorkshire 0
## 373 2020-03-07 North East and Yorkshire 0
## 374 2020-03-08 North East and Yorkshire 0
## 375 2020-03-09 North East and Yorkshire 0
## 376 2020-03-10 North East and Yorkshire 0
## 377 2020-03-11 North East and Yorkshire 0
## 378 2020-03-12 North East and Yorkshire 0
## 379 2020-03-13 North East and Yorkshire 0
## 380 2020-03-14 North East and Yorkshire 0
## 381 2020-03-15 North East and Yorkshire 2
## 382 2020-03-16 North East and Yorkshire 3
## 383 2020-03-17 North East and Yorkshire 1
## 384 2020-03-18 North East and Yorkshire 2
## 385 2020-03-19 North East and Yorkshire 6
## 386 2020-03-20 North East and Yorkshire 5
## 387 2020-03-21 North East and Yorkshire 6
## 388 2020-03-22 North East and Yorkshire 7
## 389 2020-03-23 North East and Yorkshire 9
## 390 2020-03-24 North East and Yorkshire 8
## 391 2020-03-25 North East and Yorkshire 18
## 392 2020-03-26 North East and Yorkshire 21
## 393 2020-03-27 North East and Yorkshire 28
## 394 2020-03-28 North East and Yorkshire 35
## 395 2020-03-29 North East and Yorkshire 38
## 396 2020-03-30 North East and Yorkshire 64
## 397 2020-03-31 North East and Yorkshire 60
## 398 2020-04-01 North East and Yorkshire 67
## 399 2020-04-02 North East and Yorkshire 74
## 400 2020-04-03 North East and Yorkshire 100
## 401 2020-04-04 North East and Yorkshire 105
## 402 2020-04-05 North East and Yorkshire 92
## 403 2020-04-06 North East and Yorkshire 96
## 404 2020-04-07 North East and Yorkshire 102
## 405 2020-04-08 North East and Yorkshire 107
## 406 2020-04-09 North East and Yorkshire 111
## 407 2020-04-10 North East and Yorkshire 117
## 408 2020-04-11 North East and Yorkshire 98
## 409 2020-04-12 North East and Yorkshire 84
## 410 2020-04-13 North East and Yorkshire 94
## 411 2020-04-14 North East and Yorkshire 107
## 412 2020-04-15 North East and Yorkshire 96
## 413 2020-04-16 North East and Yorkshire 103
## 414 2020-04-17 North East and Yorkshire 88
## 415 2020-04-18 North East and Yorkshire 95
## 416 2020-04-19 North East and Yorkshire 88
## 417 2020-04-20 North East and Yorkshire 100
## 418 2020-04-21 North East and Yorkshire 76
## 419 2020-04-22 North East and Yorkshire 84
## 420 2020-04-23 North East and Yorkshire 63
## 421 2020-04-24 North East and Yorkshire 72
## 422 2020-04-25 North East and Yorkshire 69
## 423 2020-04-26 North East and Yorkshire 65
## 424 2020-04-27 North East and Yorkshire 65
## 425 2020-04-28 North East and Yorkshire 57
## 426 2020-04-29 North East and Yorkshire 69
## 427 2020-04-30 North East and Yorkshire 57
## 428 2020-05-01 North East and Yorkshire 64
## 429 2020-05-02 North East and Yorkshire 48
## 430 2020-05-03 North East and Yorkshire 40
## 431 2020-05-04 North East and Yorkshire 49
## 432 2020-05-05 North East and Yorkshire 40
## 433 2020-05-06 North East and Yorkshire 51
## 434 2020-05-07 North East and Yorkshire 45
## 435 2020-05-08 North East and Yorkshire 42
## 436 2020-05-09 North East and Yorkshire 44
## 437 2020-05-10 North East and Yorkshire 40
## 438 2020-05-11 North East and Yorkshire 29
## 439 2020-05-12 North East and Yorkshire 27
## 440 2020-05-13 North East and Yorkshire 28
## 441 2020-05-14 North East and Yorkshire 31
## 442 2020-05-15 North East and Yorkshire 32
## 443 2020-05-16 North East and Yorkshire 35
## 444 2020-05-17 North East and Yorkshire 26
## 445 2020-05-18 North East and Yorkshire 30
## 446 2020-05-19 North East and Yorkshire 27
## 447 2020-05-20 North East and Yorkshire 22
## 448 2020-05-21 North East and Yorkshire 33
## 449 2020-05-22 North East and Yorkshire 22
## 450 2020-05-23 North East and Yorkshire 18
## 451 2020-05-24 North East and Yorkshire 26
## 452 2020-05-25 North East and Yorkshire 21
## 453 2020-05-26 North East and Yorkshire 21
## 454 2020-05-27 North East and Yorkshire 22
## 455 2020-05-28 North East and Yorkshire 21
## 456 2020-05-29 North East and Yorkshire 25
## 457 2020-05-30 North East and Yorkshire 20
## 458 2020-05-31 North East and Yorkshire 20
## 459 2020-06-01 North East and Yorkshire 17
## 460 2020-06-02 North East and Yorkshire 23
## 461 2020-06-03 North East and Yorkshire 23
## 462 2020-06-04 North East and Yorkshire 17
## 463 2020-06-05 North East and Yorkshire 18
## 464 2020-06-06 North East and Yorkshire 21
## 465 2020-06-07 North East and Yorkshire 14
## 466 2020-06-08 North East and Yorkshire 11
## 467 2020-06-09 North East and Yorkshire 12
## 468 2020-06-10 North East and Yorkshire 18
## 469 2020-06-11 North East and Yorkshire 7
## 470 2020-06-12 North East and Yorkshire 9
## 471 2020-06-13 North East and Yorkshire 10
## 472 2020-06-14 North East and Yorkshire 11
## 473 2020-06-15 North East and Yorkshire 9
## 474 2020-06-16 North East and Yorkshire 10
## 475 2020-06-17 North East and Yorkshire 9
## 476 2020-06-18 North East and Yorkshire 10
## 477 2020-06-19 North East and Yorkshire 6
## 478 2020-06-20 North East and Yorkshire 4
## 479 2020-06-21 North East and Yorkshire 4
## 480 2020-06-22 North East and Yorkshire 6
## 481 2020-06-23 North East and Yorkshire 7
## 482 2020-06-24 North East and Yorkshire 9
## 483 2020-06-25 North East and Yorkshire 3
## 484 2020-06-26 North East and Yorkshire 7
## 485 2020-06-27 North East and Yorkshire 3
## 486 2020-06-28 North East and Yorkshire 4
## 487 2020-06-29 North East and Yorkshire 2
## 488 2020-06-30 North East and Yorkshire 1
## 489 2020-03-01 North West 0
## 490 2020-03-02 North West 0
## 491 2020-03-03 North West 0
## 492 2020-03-04 North West 0
## 493 2020-03-05 North West 1
## 494 2020-03-06 North West 0
## 495 2020-03-07 North West 0
## 496 2020-03-08 North West 1
## 497 2020-03-09 North West 0
## 498 2020-03-10 North West 0
## 499 2020-03-11 North West 0
## 500 2020-03-12 North West 2
## 501 2020-03-13 North West 3
## 502 2020-03-14 North West 1
## 503 2020-03-15 North West 4
## 504 2020-03-16 North West 2
## 505 2020-03-17 North West 4
## 506 2020-03-18 North West 6
## 507 2020-03-19 North West 7
## 508 2020-03-20 North West 10
## 509 2020-03-21 North West 11
## 510 2020-03-22 North West 13
## 511 2020-03-23 North West 15
## 512 2020-03-24 North West 21
## 513 2020-03-25 North West 21
## 514 2020-03-26 North West 29
## 515 2020-03-27 North West 36
## 516 2020-03-28 North West 28
## 517 2020-03-29 North West 46
## 518 2020-03-30 North West 67
## 519 2020-03-31 North West 52
## 520 2020-04-01 North West 86
## 521 2020-04-02 North West 96
## 522 2020-04-03 North West 95
## 523 2020-04-04 North West 98
## 524 2020-04-05 North West 102
## 525 2020-04-06 North West 100
## 526 2020-04-07 North West 135
## 527 2020-04-08 North West 127
## 528 2020-04-09 North West 119
## 529 2020-04-10 North West 117
## 530 2020-04-11 North West 138
## 531 2020-04-12 North West 125
## 532 2020-04-13 North West 129
## 533 2020-04-14 North West 131
## 534 2020-04-15 North West 114
## 535 2020-04-16 North West 135
## 536 2020-04-17 North West 98
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## 611 2020-03-01 South East 0
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## 851 2020-06-27 South West 0
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## 854 2020-06-30 South West 0We extract the completion date from the NHS Pathways file timestamp:
The completion date of the NHS Pathways data is Wednesday 01 Jul 2020.
These are functions which will be used further in the analyses.
Function to estimate the generalised R-squared as the proportion of deviance explained by a given model:
## Function to calculate R2 for Poisson model
## not adjusted for model complexity but all models have the same DF here
Rsq <- function(x) {
1 - (x$deviance / x$null.deviance)
}Function to extract growth rates per region as well as halving times, and the associated 95% confidence intervals:
## function to extract the coefficients, find the level of the intercept,
## reconstruct the values of r, get confidence intervals
get_r <- function(model) {
## extract coefficients and conf int
out <- data.frame(r = coef(model)) %>%
rownames_to_column("var") %>%
cbind(confint(model)) %>%
filter(!grepl("day_of_week", var)) %>%
filter(grepl("day", var)) %>%
rename(lower_95 = "2.5 %",
upper_95 = "97.5 %") %>%
mutate(var = sub("day:", "", var))
## reconstruct values: intercept + region-coefficient
for (i in 2:nrow(out)) {
out[i, -1] <- out[1, -1] + out[i, -1]
}
## find the name of the intercept, restore regions names
out <- out %>%
mutate(nhs_region = model$xlevels$nhs_region) %>%
select(nhs_region, everything(), -var)
## find halving times
halving <- log(0.5) / out[,-1] %>%
rename(halving_t = r,
halving_t_lower_95 = lower_95,
halving_t_upper_95 = upper_95)
## set halving times with exclusion intervals to NA
no_halving <- out$lower_95 < 0 & out$upper_95 > 0
halving[no_halving, ] <- NA_real_
## return all data
cbind(out, halving)
}Functions used in the correlation analysis between NHS Pathways reports and deaths:
## Function to calculate Pearson's correlation between deaths and lagged
## reports. Note that `pearson` can be replaced with `spearman` for rank
## correlation.
getcor <- function(x, ndx) {
return(cor(x$deaths[ndx],
x$note_lag[ndx],
use = "complete.obs",
method = "pearson"))
}
## Catch if sample size throws an error
getcor2 <- possibly(getcor, otherwise = NA)
getboot <- function(x) {
result <- boot::boot.ci(boot::boot(x, getcor2, R = 1000),
type = "bca")
return(data.frame(n = sum(!is.na(x$note_lag) & !is.na(x$deaths)),
r = result$t0,
r_low = result$bca[4],
r_hi = result$bca[5]))
}Function to classify the day of the week into weekend, Monday, and the rest:
## Fn to add day of week
day_of_week <- function(df) {
df %>%
dplyr::mutate(day_of_week = lubridate::wday(date, label = TRUE)) %>%
dplyr::mutate(day_of_week = dplyr::case_when(
day_of_week %in% c("Sat", "Sun") ~ "weekend",
day_of_week %in% c("Mon") ~ "monday",
!(day_of_week %in% c("Sat", "Sun", "Mon")) ~ "rest_of_week"
) %>%
factor(levels = c("rest_of_week", "monday", "weekend")))
}Custom color palettes, color scales, and vectors of colors:
We look for temporal patterns in COVID-19 related 111/999 calls and 111 online reports. Analyses are broken down by NHS region. We also look for estimates of recent growth rate and associated doubling / halving time.
tab_date_region_all <- x %>%
filter(!is.na(nhs_region)) %>%
group_by(date, nhs_region) %>%
summarise(n = sum(count))
dth %>%
mutate(trusted = case_when(date_report < max(dth$date_report)-delay_max ~ "Y",
date_report >= max(dth$date_report)-delay_max ~ "N"),
value = "Deaths",
vline = max(dth$date_report)-delay_max-1,
lab = "Truncated for reporting delay",
lab_pos_x = vline + 10,
lab_pos_y = 150,
lab_col = "darkgrey") %>%
rename(date = date_report,
n = deaths) %>%
bind_rows(
mutate(tab_date_region_all, value = "Reports",
trusted = "Y",
vline = as.Date("2020-03-23"),
lab = "Start of UK lockdown",
lab_pos_x = vline - 8,
lab_pos_y = 30200,
lab_col = "black")
) %>%
mutate(value = factor(value, levels = c("Reports","Deaths"))) -> dths_reports
plot_dth_report <-
ggplot(dths_reports, aes(date, n, colour = nhs_region)) +
# Add main points and lines, coloured by region and fade out deaths for excluded period
geom_point(aes(alpha = trusted)) +
geom_line(alpha = 0.2) +
geom_smooth(method = "loess", span = .5, color = "black") +
scale_colour_manual("", values = pal) +
scale_alpha_manual(values = c(0.3,1)) +
guides(alpha = F) +
# Add vertical markers for important dates with labels - different for each facet
ggnewscale::new_scale_colour() +
geom_vline(aes(xintercept = vline, col = value), lty = "solid") +
geom_text(aes(x = lab_pos_x, y = lab_pos_y, label = lab, col = value), size = 3) +
scale_colour_manual("",values = c("black","darkgrey"), guide = F) +
# Facet by deaths and reports
facet_grid(rows = vars(value), scales = "free_y", switch = "y") +
# Other formatting
theme_bw() +
scale_weeks +
theme(legend.position = "bottom",strip.placement = "outside") +
rotate_x +
labs(x = NULL,
y = NULL)
plot_dth_reportWe plot the number of 111/999 calls and 111 online reports by age, and the proportion of 111/999 calls and 111 online reports by age. In the second graph, the vertical lines indicate the proportion of individuals residing in the corresponding NHS region who belong to the corresponding age group.
tab_date_region_age_all <- x %>%
filter(!is.na(nhs_region),
age != "missing") %>%
group_by(date, nhs_region, age) %>%
summarise(n = sum(count))
tab_date_region_age_all %>%
ggplot(aes(x = date, y = n, fill = age)) +
geom_col(position = "stack") +
scale_fill_manual(values = age.pal) +
theme_bw() +
scale_weeks +
theme(legend.position = "bottom",
axis.text.x = element_text(angle = 90, hjust = 1)) +
guides(fill = guide_legend(title = "Age", ncol = 3)) +
labs(x = NULL,
y = "Total daily reports by age") +
facet_wrap(~ nhs_region, ncol = 4)
tab_date_region_age_all <- tab_date_region_age_all %>%
group_by(date, nhs_region) %>%
summarise(tot = sum(n)) %>%
left_join(tab_date_region_age_all, by = c("date", "nhs_region")) %>%
mutate(prop_n = n/tot)
tab_date_region_age_all %>%
ggplot(aes(x = date, y = prop_n, color = age)) +
scale_color_manual(values = age.pal) +
geom_line() +
geom_point() +
geom_hline(data = nhs_region_pop, aes(yintercept = value, color = variable)) +
theme_bw() +
scale_weeks +
theme(legend.position = "bottom",
axis.text.x = element_text(angle = 90, hjust = 1)) +
guides(color = guide_legend(title = "Age", ncol = 3)) +
labs(x = NULL,
y = "Proportion of daily reports by age") +
facet_wrap(~ nhs_region, ncol = 4)We fit quasi-Poisson GLMs for 14-day windows to get growth rates over time.
## set moving time window (1/2/3 weeks)
w <- 14
# create empty df
r_all_sliding <- NULL
## make data for model
x_model_all_moving <- x %>%
filter(!is.na(nhs_region)) %>%
group_by(date, nhs_region) %>%
summarise(n = sum(count))
unique_dates <- unique(x_model_all_moving$date)
for (i in 1:(length(unique_dates) - w)) {
date_i <- unique_dates[i]
date_i_max <- date_i + w
model_data <- x_model_all_moving %>%
filter(date >= date_i & date < date_i_max) %>%
mutate(day = as.integer(date - date_i)) %>%
day_of_week()
mod <- glm(n ~ day * nhs_region + day_of_week,
data = model_data,
family = 'quasipoisson')
# get growth rate
r <- get_r(mod)
r$w_min <- date_i
r$w_max <- date_i_max
# combine all estimates
r_all_sliding <- bind_rows(r_all_sliding, r)
}
#serial interval distribution
SI_param = epitrix::gamma_mucv2shapescale(4.7, 2.9/4.7)
SI_distribution <- distcrete::distcrete("gamma", interval = 1,
shape = SI_param$shape,
scale = SI_param$scale,
w = 0.5)
#convert growth rates r to R0
r_all_sliding <- r_all_sliding %>%
mutate(R = epitrix::r2R0(r, SI_distribution),
R_lower_95 = epitrix::r2R0(lower_95, SI_distribution),
R_upper_95 = epitrix::r2R0(upper_95, SI_distribution))We examine the evolution of the growth rate by region over time.
# plot
plot_growth <-
r_all_sliding %>%
ggplot(aes(x = w_max, y = r)) +
geom_ribbon(aes(ymin = lower_95, ymax = upper_95, fill = nhs_region), alpha = 0.1) +
geom_line(aes(colour = nhs_region)) +
geom_point(aes(colour = nhs_region)) +
geom_hline(yintercept = 0, linetype = "dashed") +
theme_bw() +
scale_weeks +
theme(legend.position = "bottom",
plot.margin = margin(0.5,1,0.5,0.5, "cm")) +
guides(colour = guide_legend(title = "", override.aes = list(fill = NA)), fill = FALSE) +
labs(x = "",
y = "Estimated daily growth rate (r)") +
scale_colour_manual(values = pal)From the growth rate, we derive R and examine its value through time.
# plot
plot_R <-
r_all_sliding %>%
ggplot(aes(x = w_max, y = R)) +
geom_ribbon(aes(ymin = R_lower_95, ymax = R_upper_95, fill = nhs_region), alpha = 0.1) +
geom_line(aes(colour = nhs_region)) +
geom_point(aes(colour = nhs_region)) +
geom_hline(yintercept = 1, linetype = "dashed") +
theme_bw() +
scale_weeks +
theme(legend.position = "bottom",
plot.margin = margin(0.5,1,0.5,0.5, "cm")) +
guides(color = guide_legend(title = "", override.aes = list(fill = NA)), fill = FALSE) +
labs(x = "",
y = "Estimated effective reproduction\nnumber (Re)") +
scale_colour_manual(values = pal)
R <- r_all_sliding %>%
mutate(lower_95 = R_lower_95,
upper_95 = R_upper_95,
value = R,
measure = "R",
reference = 1)
r_R <- r_all_sliding %>%
mutate(measure = "r",
value = r,
reference = 0) %>%
bind_rows(R)
r_R %>%
ggplot(aes(x = w_max, y = value)) +
geom_ribbon(aes(ymin = lower_95, ymax = upper_95, fill = nhs_region), alpha = 0.1) +
geom_line(aes(colour = nhs_region)) +
geom_point(aes(colour = nhs_region)) +
geom_hline(aes(yintercept = reference), linetype = "dashed") +
theme_bw() +
scale_weeks +
rotate_x +
theme(legend.position = "bottom",
plot.margin = margin(0.5,1,0,0, "cm"),
strip.background = element_blank(),
# strip.text.x = element_blank(),
strip.placement = "outside"
) +
guides(color = guide_legend(title = "",
override.aes = list(fill = NA)),
fill = FALSE) +
labs(x = "", y = "") +
scale_colour_manual(values = pal) +
facet_grid(rows = vars(measure),
scales = "free_y",
switch = "y",
labeller = as_labeller(c(r = "Daily growth rate (r)",
R = "Effective reproduction\nnumber (Re)")))We repeat the above analysis, where we fit quasi-Poisson GLMs for 14-day windows to get growth rates over time, but apply this to each age group separately (0-18, 19-69, 70-120 years old).
We first run the analysis for 0-18 years old.
## set moving time window (2 weeks)
w <- 14
# create empty df
r_all_sliding_0_18 <- NULL
## make data for model
x_model_all_moving_0_18 <- x %>%
filter(!is.na(nhs_region),
age == "0-18") %>%
group_by(date, nhs_region) %>%
summarise(n = sum(count))
unique_dates <- unique(x_model_all_moving_0_18$date)
for (i in 1:(length(unique_dates) - w)) {
date_i <- unique_dates[i]
date_i_max <- date_i + w
model_data <- x_model_all_moving_0_18 %>%
filter(date >= date_i & date < date_i_max) %>%
mutate(day = as.integer(date - date_i)) %>%
day_of_week()
mod <- glm(n ~ day * nhs_region + day_of_week,
data = model_data,
family = 'quasipoisson')
# get growth rate
r <- get_r(mod)
r$w_min <- date_i
r$w_max <- date_i_max
# combine all estimates
r_all_sliding_0_18 <- bind_rows(r_all_sliding_0_18, r)
}
#serial interval distribution
SI_param = epitrix::gamma_mucv2shapescale(4.7, 2.9/4.7)
SI_distribution <- distcrete::distcrete("gamma", interval = 1,
shape = SI_param$shape,
scale = SI_param$scale, w = 0.5)
#convert growth rates r to R0
r_all_sliding_0_18 <- r_all_sliding_0_18 %>%
mutate(R = epitrix::r2R0(r, SI_distribution),
R_lower_95 = epitrix::r2R0(lower_95, SI_distribution),
R_upper_95 = epitrix::r2R0(upper_95, SI_distribution))# plot
plot_growth <-
r_all_sliding_0_18 %>%
ggplot(aes(x = w_max, y = r)) +
geom_ribbon(aes(ymin = lower_95, ymax = upper_95, fill = nhs_region), alpha = 0.1) +
geom_line(aes(colour = nhs_region)) +
geom_point(aes(colour = nhs_region)) +
geom_hline(yintercept = 0, linetype = "dashed") +
theme_bw() +
scale_weeks +
theme(legend.position = "bottom",
plot.margin = margin(0.5,1,0.5,0.5, "cm")) +
guides(colour = guide_legend(title = "",override.aes = list(fill = NA)), fill = FALSE) +
labs(x = "",
y = "Estimated daily growth rate (r)"
) +
scale_colour_manual(values = pal)# plot
plot_R <-
r_all_sliding_0_18 %>%
ggplot(aes(x = w_max, y = R)) +
geom_ribbon(aes(ymin = R_lower_95, ymax = R_upper_95, fill = nhs_region), alpha = 0.1) +
geom_line(aes(colour = nhs_region)) +
geom_point(aes(colour = nhs_region)) +
geom_hline(yintercept = 1, linetype = "dashed") +
theme_bw() +
scale_weeks +
theme(legend.position = "bottom",
plot.margin = margin(0.5,1,0.5,0.5, "cm")) +
guides(color = guide_legend(title = "", override.aes = list(fill = NA)), fill = FALSE) +
labs(x = "",
y = "Estimated effective reproduction\nnumber (Re)"
) +
scale_colour_manual(values = pal)
R <- r_all_sliding_0_18 %>%
mutate(lower_95 = R_lower_95,
upper_95 = R_upper_95,
value = R,
measure = "R",
reference = 1)
r_R <- r_all_sliding_0_18 %>%
mutate(measure = "r",
value = r,
reference = 0) %>%
bind_rows(R)
fig2_3_0_18 <- r_R %>%
ggplot(aes(x = w_max, y = value)) +
geom_ribbon(aes(ymin = lower_95, ymax = upper_95, fill = nhs_region), alpha = 0.1) +
geom_line(aes(colour = nhs_region)) +
geom_point(aes(colour = nhs_region)) +
geom_hline(aes(yintercept = reference), linetype = "dashed") +
theme_bw() +
scale_weeks +
theme(legend.position = "bottom",
plot.margin = margin(0.5,1,0,0, "cm"),
strip.background = element_blank(),
strip.placement = "outside"
) +
guides(color = guide_legend(title = "", override.aes = list(fill = NA)), fill = FALSE) +
labs(x = "", y = "") +
scale_colour_manual(values = pal) +
facet_grid(rows = vars(measure),
scales = "free_y",
switch = "y",
labeller = as_labeller(c(r = "Daily growth rate (r)",
R = "Effective reproduction\nnumber (Re)")))Then, we run the analysis for 19-69 years old.
## set moving time window (2 weeks)
w <- 14
# create empty df
r_all_sliding_19_69 <- NULL
## make data for model
x_model_all_moving_19_69 <- x %>%
filter(!is.na(nhs_region),
age == "19-69") %>%
group_by(date, nhs_region) %>%
summarise(n = sum(count))
unique_dates <- unique(x_model_all_moving_19_69$date)
for (i in 1:(length(unique_dates) - w)) {
date_i <- unique_dates[i]
date_i_max <- date_i + w
model_data <- x_model_all_moving_19_69 %>%
filter(date >= date_i & date < date_i_max) %>%
mutate(day = as.integer(date - date_i)) %>%
day_of_week()
mod <- glm(n ~ day * nhs_region + day_of_week,
data = model_data,
family = 'quasipoisson')
# get growth rate
r <- get_r(mod)
r$w_min <- date_i
r$w_max <- date_i_max
# combine all estimates
r_all_sliding_19_69 <- bind_rows(r_all_sliding_19_69, r)
}
#serial interval distribution
SI_param = epitrix::gamma_mucv2shapescale(4.7, 2.9/4.7)
SI_distribution <- distcrete::distcrete("gamma", interval = 1,
shape = SI_param$shape,
scale = SI_param$scale, w = 0.5)
#convert growth rates r to R0
r_all_sliding_19_69 <- r_all_sliding_19_69 %>%
mutate(R = epitrix::r2R0(r, SI_distribution),
R_lower_95 = epitrix::r2R0(lower_95, SI_distribution),
R_upper_95 = epitrix::r2R0(upper_95, SI_distribution))# plot
plot_growth <-
r_all_sliding_19_69 %>%
ggplot(aes(x = w_max, y = r)) +
geom_ribbon(aes(ymin = lower_95, ymax = upper_95, fill = nhs_region), alpha = 0.1) +
geom_line(aes(colour = nhs_region)) +
geom_point(aes(colour = nhs_region)) +
geom_hline(yintercept = 0, linetype = "dashed") +
theme_bw() +
scale_weeks +
theme(legend.position = "bottom",
plot.margin = margin(0.5,1,0.5,0.5, "cm")) +
guides(colour = guide_legend(title = "", override.aes = list(fill = NA)), fill = FALSE) +
labs(x = "",
y = "Estimated daily growth rate (r)") +
scale_colour_manual(values = pal)# plot
plot_R <-
r_all_sliding_19_69 %>%
ggplot(aes(x = w_max, y = R)) +
geom_ribbon(aes(ymin = R_lower_95, ymax = R_upper_95, fill = nhs_region), alpha = 0.1) +
geom_line(aes(colour = nhs_region)) +
geom_point(aes(colour = nhs_region)) +
geom_hline(yintercept = 1, linetype = "dashed") +
theme_bw() +
scale_weeks +
theme(legend.position = "bottom",
plot.margin = margin(0.5,1,0.5,0.5, "cm")) +
guides(color = guide_legend(title = "", override.aes = list(fill = NA)), fill = FALSE) +
labs(x = "",
y = "Estimated effective reproduction\nnumber (Re)"
) +
scale_colour_manual(values = pal)
R <- r_all_sliding_19_69 %>%
mutate(lower_95 = R_lower_95,
upper_95 = R_upper_95,
value = R,
measure = "R",
reference = 1)
r_R <- r_all_sliding_19_69 %>%
mutate(measure = "r",
value = r,
reference = 0) %>%
bind_rows(R)
fig2_3_19_69 <- r_R %>%
ggplot(aes(x = w_max, y = value)) +
geom_ribbon(aes(ymin = lower_95, ymax = upper_95, fill = nhs_region), alpha = 0.1) +
geom_line(aes(colour = nhs_region)) +
geom_point(aes(colour = nhs_region)) +
geom_hline(aes(yintercept = reference), linetype = "dashed") +
theme_bw() +
scale_weeks +
theme(legend.position = "bottom",
plot.margin = margin(0.5,1,0,0, "cm"),
strip.background = element_blank(),
strip.placement = "outside"
) +
guides(color = guide_legend(title = "", override.aes = list(fill = NA)), fill = FALSE) +
labs(x = "", y = "") +
scale_colour_manual(values = pal) +
facet_grid(rows = vars(measure),
scales = "free_y",
switch = "y",
labeller = as_labeller(c(r = "Daily growth rate (r)",
R = "Effective reproduction\nnumber (Re)")))Finally, we run the analysis for 70-120 years old.
## set moving time window (2 weeks)
w <- 14
# create empty df
r_all_sliding_70_120 <- NULL
## make data for model
x_model_all_moving_70_120 <- x %>%
filter(!is.na(nhs_region),
age == "70-120") %>%
group_by(date, nhs_region) %>%
summarise(n = sum(count))
unique_dates <- unique(x_model_all_moving_70_120$date)
for (i in 1:(length(unique_dates) - w)) {
date_i <- unique_dates[i]
date_i_max <- date_i + w
model_data <- x_model_all_moving_70_120 %>%
filter(date >= date_i & date < date_i_max) %>%
mutate(day = as.integer(date - date_i)) %>%
day_of_week()
mod <- glm(n ~ day * nhs_region + day_of_week,
data = model_data,
family = 'quasipoisson')
# get growth rate
r <- get_r(mod)
r$w_min <- date_i
r$w_max <- date_i_max
# combine all estimates
r_all_sliding_70_120 <- bind_rows(r_all_sliding_70_120, r)
}
#serial interval distribution
SI_param = epitrix::gamma_mucv2shapescale(4.7, 2.9/4.7)
SI_distribution <- distcrete::distcrete("gamma", interval = 1,
shape = SI_param$shape,
scale = SI_param$scale, w = 0.5)
#convert growth rates r to R0
r_all_sliding_70_120 <- r_all_sliding_70_120 %>%
mutate(R = epitrix::r2R0(r, SI_distribution),
R_lower_95 = epitrix::r2R0(lower_95, SI_distribution),
R_upper_95 = epitrix::r2R0(upper_95, SI_distribution))# plot
plot_growth <-
r_all_sliding_70_120 %>%
ggplot(aes(x = w_max, y = r)) +
geom_ribbon(aes(ymin = lower_95, ymax = upper_95, fill = nhs_region), alpha = 0.1) +
geom_line(aes(colour = nhs_region)) +
geom_point(aes(colour = nhs_region)) +
geom_hline(yintercept = 0, linetype = "dashed") +
theme_bw() +
scale_weeks +
theme(legend.position = "bottom",
plot.margin = margin(0.5,1,0.5,0.5, "cm")) +
guides(colour = guide_legend(title = "",override.aes = list(fill = NA)), fill = FALSE) +
labs(x = "",
y = "Estimated daily growth rate (r)"
) +
scale_colour_manual(values = pal)# plot
plot_R <-
r_all_sliding_70_120 %>%
ggplot(aes(x = w_max, y = R)) +
geom_ribbon(aes(ymin = R_lower_95, ymax = R_upper_95, fill = nhs_region), alpha = 0.1) +
geom_line(aes(colour = nhs_region)) +
geom_point(aes(colour = nhs_region)) +
geom_hline(yintercept = 1, linetype = "dashed") +
theme_bw() +
scale_weeks +
theme(legend.position = "bottom",
plot.margin = margin(0.5,1,0.5,0.5, "cm")) +
guides(color = guide_legend(title = "", override.aes = list(fill = NA)), fill = FALSE) +
labs(x = "",
y = "Estimated effective reproduction\nnumber (Re)") +
scale_colour_manual(values = pal)
R <- r_all_sliding_70_120 %>%
mutate(lower_95 = R_lower_95,
upper_95 = R_upper_95,
value = R,
measure = "R",
reference = 1)
r_R <- r_all_sliding_70_120 %>%
mutate(measure = "r",
value = r,
reference = 0) %>%
bind_rows(R)
fig2_3_70_120 <- r_R %>%
ggplot(aes(x = w_max, y = value)) +
geom_ribbon(aes(ymin = lower_95, ymax = upper_95, fill = nhs_region), alpha = 0.1) +
geom_line(aes(colour = nhs_region)) +
geom_point(aes(colour = nhs_region)) +
geom_hline(aes(yintercept = reference), linetype = "dashed") +
theme_bw() +
scale_weeks +
theme(legend.position = "bottom",
plot.margin = margin(0.5,1,0,0, "cm"),
strip.background = element_blank(),
strip.placement = "outside"
) +
guides(color = guide_legend(title = "", override.aes = list(fill = NA)), fill = FALSE) +
labs(x = "", y = "") +
scale_colour_manual(values = pal) +
facet_grid(rows = vars(measure),
scales = "free_y",
switch = "y",
labeller = as_labeller(c(r = "Daily growth rate (r)",
R = "Effective reproduction\nnumber (Re)"))) We combine the estimated growth rates and effective reproduction numbers into a single figure.
ggpubr::ggarrange(fig2_3_0_18,
fig2_3_19_69,
fig2_3_70_120,
nrow = 3,
labels = "AUTO",
common.legend = TRUE,
legend = "bottom",
align = "hv") We want to explore the correlation between NHS Pathways reports and deaths, and assess the potential for reports to be used as an early warning system for disease resurgence.
Death data are publically available. We truncate the time series to avoid bias from reporting delay - we assume a conservative delay of three weeks.
We calculate Pearson’s correlation coefficient between deaths and NHS Pathways notifications using different lags. Confidence intervals are obtained using bootstrap. Note that results were also confirmed using Spearman’s rank correlation.
First we join the NHS Pathways and death data, and aggregate over all England:
## truncate death data for reporting delay
trunc_date <- max(dth$date_report) - delay_max
dth_trunc <- dth %>%
rename(date = date_report) %>%
filter(date <= trunc_date)
## join with notification data
all_data <- x %>%
filter(!is.na(nhs_region)) %>%
group_by(date, nhs_region) %>%
summarise(count = sum(count, na.rm = T)) %>%
ungroup %>%
inner_join(dth_trunc,
by = c("date","nhs_region"))
all_tot <- all_data %>%
group_by(date) %>%
summarise(count = sum(count, na.rm = TRUE),
deaths = sum(deaths, na.rm = TRUE)) We calculate correlation with lagged NHS Pathways reports from 0 to 30 days behind deaths:
## Calculate all correlations + bootstrap CIs
lag_cor <- data.frame()
for (i in 0:30) {
## lag reports
summary <- all_tot %>%
mutate(note_lag = lag(count, i)) %>%
## calculate rank correlation and bootstrap CI
getboot(.) %>%
mutate(lag = i)
lag_cor <- bind_rows(lag_cor, summary)
}
cor_vs_lag <- ggplot(lag_cor, aes(lag, r)) +
theme_bw() +
geom_ribbon(aes(ymin = r_low, ymax = r_hi), alpha = 0.2) +
geom_hline(yintercept = 0, lty = "longdash") +
geom_point() +
geom_line() +
labs(x = "Lag between NHS pathways and death data (days)",
y = "Pearson's correlation") +
large_txt
cor_vs_lagThis analysis suggests that the best lag is 23 days. We then compare and plot the number of deaths reported against the number of NHS Pathways reports lagged by 23 days.
all_tot <- all_tot %>%
rename(date_death = date) %>%
mutate(note_lag = lag(count, lag_cor$lag[l_opt]),
note_lag_c = (note_lag - mean(note_lag, na.rm = T)),
date_note = lag(date_death,16))
lag_mod <- glm(deaths ~ note_lag, data = all_tot, family = "quasipoisson")
summary(lag_mod)
##
## Call:
## glm(formula = deaths ~ note_lag, family = "quasipoisson", data = all_tot)
##
## Deviance Residuals:
## Min 1Q Median 3Q Max
## -11.0567 -3.3446 -0.3257 3.8621 6.4158
##
## Coefficients:
## Estimate Std. Error t value Pr(>|t|)
## (Intercept) 4.795e+00 5.653e-02 84.83 <2e-16 ***
## note_lag 1.288e-05 5.800e-07 22.21 <2e-16 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## (Dispersion parameter for quasipoisson family taken to be 15.65601)
##
## Null deviance: 8243.52 on 60 degrees of freedom
## Residual deviance: 958.51 on 59 degrees of freedom
## (23 observations deleted due to missingness)
## AIC: NA
##
## Number of Fisher Scoring iterations: 4
exp(coefficients(lag_mod))
## (Intercept) note_lag
## 120.921157 1.000013
exp(confint(lag_mod))
## 2.5 % 97.5 %
## (Intercept) 108.086338 134.902664
## note_lag 1.000012 1.000014
Rsq(lag_mod)
## [1] 0.8837254
mod_fit <- as.data.frame(predict(lag_mod, type = "link", se.fit = TRUE)[1:2])
all_tot_pred <-
all_tot %>%
filter(!is.na(note_lag)) %>%
mutate(pred = mod_fit$fit,
pred.se = mod_fit$se.fit,
low = exp(pred - 1.96*pred.se),
hi = exp(pred + 1.96*pred.se))
glm_fit <- all_tot_pred %>%
filter(!is.na(note_lag)) %>%
ggplot(aes(x = note_lag, y = deaths)) +
geom_point() +
geom_line(aes(y = exp(pred))) +
geom_ribbon(aes(ymin = low, ymax = hi), alpha = 0.3, col = "grey") +
theme_bw() +
labs(y = "Daily number of\ndeaths reported",
x = "Daily number of NHS Pathways reports") +
large_txt
glm_fitThis is a comparison of gamma versus lognormal distribution for the serial interval used to convert r to R in our analysis. Both distributions are parameterised with mean 4.7 and standard deviation 2.9.
SI_param <- epitrix::gamma_mucv2shapescale(4.7, 2.9/4.7)
SI_distribution <- distcrete::distcrete("gamma", interval = 1,
shape = SI_param$shape,
scale = SI_param$scale, w = 0.5)
SI_distribution2 <- distcrete::distcrete("lnorm", interval = 1,
meanlog = log(4.7),
sdlog = log(2.9), w = 0.5)
SI_dist1 <- data.frame(x = SI_distribution$r(1e5))
SI_dist1 <- count(SI_dist1, x) %>%
ggplot() +
geom_col(aes(x = x, y = n)) +
labs(x = "Serial interval (days)", y = "Frequency") +
scale_x_continuous(breaks = seq(0, 30, 5)) +
theme_bw()
SI_dist2 <- data.frame(x = SI_distribution2$r(1e5))
SI_dist2 <- count(SI_dist2, x) %>%
ggplot() +
geom_col(aes(x = x, y = n)) +
labs(x = "Serial interval (days)", y = "Frequency") +
scale_x_continuous(breaks = seq(0, 200, 20), limits = c(0, 200)) +
theme_bw()
ggpubr::ggarrange(SI_dist1,
SI_dist2,
nrow = 1,
labels = "AUTO") We reproduce the window analysis with either a 7 or 21 days window for sensitivity purposes.
First with the 7 days window:
## set moving time window (1/2/3 weeks)
w <- 7
# create empty df
r_all_sliding_7days <- NULL
## make data for model
x_model_all_moving <- x %>%
filter(!is.na(nhs_region)) %>%
group_by(date, nhs_region) %>%
summarise(n = sum(count))
unique_dates <- unique(x_model_all_moving$date)
for (i in 1:(length(unique_dates) - w)) {
date_i <- unique_dates[i]
date_i_max <- date_i + w
model_data <- x_model_all_moving %>%
filter(date >= date_i & date < date_i_max) %>%
mutate(day = as.integer(date - date_i)) %>%
day_of_week()
mod <- glm(n ~ day * nhs_region + day_of_week,
data = model_data,
family = 'quasipoisson')
# get growth rate
r <- get_r(mod)
r$w_min <- date_i
r$w_max <- date_i_max
# combine all estimates
r_all_sliding_7days <- bind_rows(r_all_sliding_7days, r)
}
#serial interval distribution
SI_param = epitrix::gamma_mucv2shapescale(4.7, 2.9/4.7)
SI_distribution <- distcrete::distcrete("gamma", interval = 1,
shape = SI_param$shape,
scale = SI_param$scale,
w = 0.5)
#convert growth rates r to R0
r_all_sliding_7days <- r_all_sliding_7days %>%
mutate(R = epitrix::r2R0(r, SI_distribution),
R_lower_95 = epitrix::r2R0(lower_95, SI_distribution),
R_upper_95 = epitrix::r2R0(upper_95, SI_distribution))# plot
plot_growth <-
r_all_sliding_7days %>%
ggplot(aes(x = w_max, y = r)) +
geom_ribbon(aes(ymin = lower_95, ymax = upper_95, fill = nhs_region), alpha = 0.1) +
geom_line(aes(colour = nhs_region)) +
geom_point(aes(colour = nhs_region)) +
geom_hline(yintercept = 0, linetype = "dashed") +
theme_bw() +
scale_weeks +
theme(legend.position = "bottom",
plot.margin = margin(0.5,1,0.5,0.5, "cm")) +
guides(colour = guide_legend(title = "",override.aes = list(fill = NA)), fill = FALSE) +
labs(x = "",
y = "Estimated daily growth rate (r)") +
scale_colour_manual(values = pal)plot_R <- r_all_sliding_7days %>%
ggplot(aes(x = w_max, y = R)) +
geom_ribbon(aes(ymin = R_lower_95, ymax = R_upper_95, fill = nhs_region), alpha = 0.1) +
geom_line(aes(colour = nhs_region)) +
geom_point(aes(colour = nhs_region)) +
geom_hline(yintercept = 1, linetype = "dashed") +
theme_bw() +
scale_weeks +
theme(legend.position = "bottom",
plot.margin = margin(0.5,1,0.5,0.5, "cm")) +
guides(color = guide_legend(title = "", override.aes = list(fill = NA)), fill = FALSE) +
labs(x = "",
y = "Estimated effective reproduction\nnumber (Re)") +
scale_colour_manual(values = pal)
R <- r_all_sliding_7days %>%
mutate(lower_95 = R_lower_95,
upper_95 = R_upper_95,
value = R,
measure = "R",
reference = 1)
r_R <- r_all_sliding_7days %>%
mutate(measure = "r",
value = r,
reference = 0) %>%
bind_rows(R)
r_R_7 <- r_R %>%
ggplot(aes(x = w_max, y = value)) +
geom_ribbon(aes(ymin = lower_95, ymax = upper_95, fill = nhs_region), alpha = 0.1) +
geom_line(aes(colour = nhs_region)) +
geom_point(aes(colour = nhs_region)) +
geom_hline(aes(yintercept = reference), linetype = "dashed") +
theme_bw() +
scale_weeks +
theme(legend.position = "bottom",
plot.margin = margin(0.5,1,0,0, "cm"),
strip.background = element_blank(),
strip.placement = "outside"
) +
guides(color = guide_legend(title = "", override.aes = list(fill = NA)), fill = FALSE) +
labs(x = "", y = "") +
scale_colour_manual(values = pal) +
facet_grid(rows = vars(measure),
scales = "free_y",
switch = "y",
labeller = as_labeller(c(r = "Daily growth rate (r)",
R = "Effective reproduction\nnumber (Re)")))Then with the 21 days window:
## set moving time window (1/2/3 weeks)
w <- 21
# create empty df
r_all_sliding_21days <- NULL
## make data for model
x_model_all_moving <- x %>%
filter(!is.na(nhs_region)) %>%
group_by(date, nhs_region) %>%
summarise(n = sum(count))
unique_dates <- unique(x_model_all_moving$date)
for (i in 1:(length(unique_dates) - w)) {
date_i <- unique_dates[i]
date_i_max <- date_i + w
model_data <- x_model_all_moving %>%
filter(date >= date_i & date < date_i_max) %>%
mutate(day = as.integer(date - date_i)) %>%
day_of_week()
mod <- glm(n ~ day * nhs_region + day_of_week,
data = model_data,
family = 'quasipoisson')
# get growth rate
r <- get_r(mod)
r$w_min <- date_i
r$w_max <- date_i_max
# combine all estimates
r_all_sliding_21days <- bind_rows(r_all_sliding_21days, r)
}
#serial interval distribution
SI_param = epitrix::gamma_mucv2shapescale(4.7, 2.9/4.7)
SI_distribution <- distcrete::distcrete("gamma", interval = 1,
shape = SI_param$shape,
scale = SI_param$scale,
w = 0.5)
#convert growth rates r to R0
r_all_sliding_21days <- r_all_sliding_21days %>%
mutate(R = epitrix::r2R0(r, SI_distribution),
R_lower_95 = epitrix::r2R0(lower_95, SI_distribution),
R_upper_95 = epitrix::r2R0(upper_95, SI_distribution))# plot
plot_growth <-
r_all_sliding_21days %>%
ggplot(aes(x = w_max, y = r)) +
geom_ribbon(aes(ymin = lower_95, ymax = upper_95, fill = nhs_region), alpha = 0.1) +
geom_line(aes(colour = nhs_region)) +
geom_point(aes(colour = nhs_region)) +
geom_hline(yintercept = 0, linetype = "dashed") +
theme_bw() +
scale_weeks +
theme(legend.position = "bottom",
plot.margin = margin(0.5,1,0.5,0.5, "cm")) +
guides(colour = guide_legend(title = "",override.aes = list(fill = NA)), fill = FALSE) +
labs(x = "",
y = "Estimated daily growth rate (r)") +
scale_colour_manual(values = pal)# plot
plot_R <-
r_all_sliding_21days %>%
ggplot(aes(x = w_max, y = R)) +
geom_ribbon(aes(ymin = R_lower_95, ymax = R_upper_95, fill = nhs_region), alpha = 0.1) +
geom_line(aes(colour = nhs_region)) +
geom_point(aes(colour = nhs_region)) +
geom_hline(yintercept = 1, linetype = "dashed") +
theme_bw() +
scale_weeks +
theme(legend.position = "bottom",
plot.margin = margin(0.5,1,0.5,0.5, "cm")) +
guides(color = guide_legend(title = "", override.aes = list(fill = NA)), fill = FALSE) +
labs(x = "",
y = "Estimated effective reproduction\nnumber (Re)") +
scale_colour_manual(values = pal)
R <- r_all_sliding_21days %>%
mutate(lower_95 = R_lower_95,
upper_95 = R_upper_95,
value = R,
measure = "R",
reference = 1)
r_R <- r_all_sliding_21days %>%
mutate(measure = "r",
value = r,
reference = 0) %>%
bind_rows(R)
r_R_21 <- r_R %>%
ggplot(aes(x = w_max, y = value)) +
geom_ribbon(aes(ymin = lower_95, ymax = upper_95, fill = nhs_region), alpha = 0.1) +
geom_line(aes(colour = nhs_region)) +
geom_point(aes(colour = nhs_region)) +
geom_hline(aes(yintercept = reference), linetype = "dashed") +
theme_bw() +
scale_weeks +
theme(legend.position = "bottom",
plot.margin = margin(0.5,1,0,0, "cm"),
strip.background = element_blank(),
strip.placement = "outside"
) +
guides(color = guide_legend(title = "", override.aes = list(fill = NA)), fill = FALSE) +
labs(x = "", y = "") +
scale_colour_manual(values = pal) +
facet_grid(rows = vars(measure),
scales = "free_y",
switch = "y",
labeller = as_labeller(c(r = "Daily growth rate (r)",
R = "Effective reproduction\nnumber (Re)")))And we combine both outputs into a single plot:
ggpubr::ggarrange(r_R_7,
r_R_21,
nrow = 2,
labels = "AUTO",
common.legend = TRUE,
legend = "bottom")
lag_cor_reg <- data.frame()
for (i in 0:30) {
summary <-
all_data %>%
group_by(nhs_region) %>%
mutate(note_lag = lag(count, i)) %>%
## calculate rank correlation and bootstrap CI for each region
group_modify(~getboot(.x)) %>%
mutate(lag = i)
lag_cor_reg <- bind_rows(lag_cor_reg, summary)
}
cor_vs_lag_reg <-
lag_cor_reg %>%
ggplot(aes(lag, r, col = nhs_region)) +
geom_hline(yintercept = 0, lty = "longdash") +
geom_ribbon(aes(ymin = r_low, ymax = r_hi, col = NULL, fill = nhs_region), alpha = 0.2) +
geom_point() +
geom_line() +
facet_wrap(~nhs_region) +
scale_color_manual(values = pal) +
scale_fill_manual(values = pal, guide = F) +
theme_bw() +
labs(x = "Lag between NHS pathways and death data (days)", y = "Pearson's correlation", col = "NHS region") +
theme(legend.position = "bottom") +
guides(color = guide_legend(override.aes = list(fill = NA)))
cor_vs_lag_regWe save the tables created during our analysis:
if (!dir.exists("excel_tables")) {
dir.create("excel_tables")
}
## list all tables, and loop over export
tables_to_export <- c("r_all_sliding", "lag_cor")
for (e in tables_to_export) {
rio::export(get(e),
file.path("excel_tables",
paste0(e, ".xlsx")))
}
## also export result from regression on lagged data
rio::export(lag_mod, file.path("excel_tables", "lag_mod.rds"))The following information documents the system on which the document was compiled.
This provides information on the operating system.
This provides information on the version of R used:
This provides information on the packages used:
sessionInfo()
## R version 4.0.2 (2020-06-22)
## Platform: x86_64-apple-darwin17.0 (64-bit)
## Running under: macOS Catalina 10.15.5
##
## Matrix products: default
## BLAS: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRblas.dylib
## LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib
##
## locale:
## [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
##
## attached base packages:
## [1] stats graphics grDevices utils datasets methods base
##
## other attached packages:
## [1] ggnewscale_0.4.1 ggpubr_0.4.0 lubridate_1.7.9
## [4] chngpt_2020.5-21 cyphr_1.1.0 DT_0.14
## [7] kableExtra_1.1.0 janitor_2.0.1 remotes_2.1.1
## [10] projections_0.5.1 earlyR_0.0.1 epitrix_0.2.2
## [13] distcrete_1.0.3 incidence_1.7.1 rio_0.5.16
## [16] reshape2_1.4.4 rvest_0.3.5 xml2_1.3.2
## [19] linelist_0.0.40.9000 forcats_0.5.0 stringr_1.4.0
## [22] dplyr_1.0.0 purrr_0.3.4 readr_1.3.1
## [25] tidyr_1.1.0 tibble_3.0.1 ggplot2_3.3.2
## [28] tidyverse_1.3.0 here_0.1 reportfactory_0.0.5
##
## loaded via a namespace (and not attached):
## [1] nlme_3.1-148 fs_1.4.2 webshot_0.5.2 httr_1.4.1
## [5] rprojroot_1.3-2 tools_4.0.2 backports_1.1.8 utf8_1.1.4
## [9] R6_2.4.1 mgcv_1.8-31 DBI_1.1.0 colorspace_1.4-1
## [13] withr_2.2.0 gridExtra_2.3 tidyselect_1.1.0 sodium_1.1
## [17] curl_4.3 compiler_4.0.2 cli_2.0.2 labeling_0.3
## [21] matchmaker_0.1.1 scales_1.1.1 digest_0.6.25 foreign_0.8-80
## [25] rmarkdown_2.3 pkgconfig_2.0.3 htmltools_0.5.0 dbplyr_1.4.4
## [29] htmlwidgets_1.5.1 rlang_0.4.6 readxl_1.3.1 rstudioapi_0.11
## [33] farver_2.0.3 generics_0.0.2 jsonlite_1.7.0 crosstalk_1.1.0.1
## [37] car_3.0-8 zip_2.0.4 kyotil_2019.11-22 magrittr_1.5
## [41] Matrix_1.2-18 Rcpp_1.0.4.6 munsell_0.5.0 fansi_0.4.1
## [45] viridis_0.5.1 abind_1.4-5 lifecycle_0.2.0 stringi_1.4.6
## [49] yaml_2.2.1 carData_3.0-4 snakecase_0.11.0 MASS_7.3-51.6
## [53] plyr_1.8.6 grid_4.0.2 blob_1.2.1 crayon_1.3.4
## [57] lattice_0.20-41 cowplot_1.0.0 splines_4.0.2 haven_2.3.1
## [61] hms_0.5.3 knitr_1.29 pillar_1.4.4 boot_1.3-25
## [65] ggsignif_0.6.0 reprex_0.3.0 glue_1.4.1 evaluate_0.14
## [69] data.table_1.12.8 modelr_0.1.8 vctrs_0.3.1 selectr_0.4-2
## [73] cellranger_1.1.0 gtable_0.3.0 assertthat_0.2.1 xfun_0.15
## [77] openxlsx_4.1.5 broom_0.5.6 rstatix_0.6.0 survival_3.1-12
## [81] viridisLite_0.3.0 ellipsis_0.3.1